--- a/GO-enrich.R	Thu Jun 27 04:06:45 2019 -0400
+++ b/GO-enrich.R	Thu Jun 27 09:44:07 2019 -0400
@@ -44,7 +44,7 @@
   return (width)
 }
 
-repartition.GO <- function(geneid, orgdb, ontology, level=3, readable=TRUE) {
+repartition_GO <- function(geneid, orgdb, ontology, level=3, readable=TRUE, plot) {
   ggo<-groupGO(gene=geneid, 
                OrgDb = orgdb, 
                ont=ontology, 
@@ -55,18 +55,30 @@
     ggo@result$Description <- sapply(as.vector(ggo@result$Description), function(x) {ifelse(nchar(x)>50, substr(x,1,50),x)},USE.NAMES = FALSE)
     #nb_max_char = max_str_length_10_first(ggo$Description)
     #width = width_by_max_char(nb_max_char)
-    name <- paste("GGO_", ontology, "_bar-plot", sep = "")
-    png(name,height = 720, width = 600)
-    p <- barplot(ggo, showCategory=10)
-    print(p)
-    dev.off()
+    
+    if ("dotplot" %in% plot ){
+      dot_name <- paste("GGO_", ontology, "_dot-plot", sep = "")
+      png(dot_name,height = 720, width = 600)
+      p <- dotplot(ggo, showCategory=10)
+      print(p)
+      dev.off()
+    }
+    
+    if ("barplot" %in% plot ){
+      bar_name <- paste("GGO_", ontology, "_bar-plot", sep = "")
+      png(bar_name,height = 720, width = 600)
+      p <- barplot(ggo, showCategory=10)
+      print(p)
+      dev.off()
+    }
+
     ggo <- as.data.frame(ggo)
     return(ggo)
   }
 }
 
 # GO over-representation test
-enrich.GO <- function(geneid, universe, orgdb, ontology, pval_cutoff, qval_cutoff,plot) {
+enrich_GO <- function(geneid, universe, orgdb, ontology, pval_cutoff, qval_cutoff,plot) {
   ego<-enrichGO(gene=geneid,
                 universe=universe,
                 OrgDb=orgdb,
@@ -126,7 +138,7 @@
   }
 }
 
-clusterProfiler = function() {
+get_args <- function(){
   args <- commandArgs(TRUE)
   if(length(args)<1) {
     args <- c("--help")
@@ -162,10 +174,18 @@
   args <- as.list(as.character(argsDF$V2))
   names(args) <- argsDF$V1
   
+  return(args)
+}
+
+
+main <- function() {
+  
+  #get args from command
+  args <- get_args()
+
   #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
   #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
   
-  
   go_represent=str2bool(args$go_represent)
   go_enrich=str2bool(args$go_enrich)
   if (go_enrich){
@@ -272,17 +292,19 @@
     universe_gene = NULL
   }
 
+  print(plot)
+  
   ##enrichGO : GO over-representation test
   for (onto in ontology) {
     if (go_represent) {
-      ggo<-repartition.GO(gene, orgdb, onto, level, readable=TRUE)
+      ggo<-repartition_GO(gene, orgdb, onto, level, readable=TRUE,plot)
       if (is.list(ggo)){ggo <- as.data.frame(apply(ggo, c(1,2), function(x) gsub("^$|^ $", NA, x)))}  #convert "" and " " to NA
       output_path = paste("cluster_profiler_GGO_",onto,".tsv",sep="")
       write.table(ggo, output_path, sep="\t", row.names = FALSE, quote = FALSE )
     }
 
     if (go_enrich) {
-      ego<-enrich.GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot)
+      ego<-enrich_GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot)
       if (is.list(ego)){ego <- as.data.frame(apply(ego, c(1,2), function(x) gsub("^$|^ $", NA, x)))}  #convert "" and " " to NA
       output_path = paste("cluster_profiler_EGO_",onto,".tsv",sep="")
       write.table(ego, output_path, sep="\t", row.names = FALSE, quote = FALSE )
@@ -290,4 +312,6 @@
   }
 }
 
-clusterProfiler()
+if(!interactive()) {
+  main()
+}

--- a/cluster_profiler.xml	Thu Jun 27 04:06:45 2019 -0400
+++ b/cluster_profiler.xml	Thu Jun 27 09:44:07 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.06.27">
+<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.06.27.1">
     <description>(Human, Mouse, Rat)[clusterProfiler]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>